Prepare

Structure preparation module for the Rush Python client.

Usage:

from rush import prepare

# Protein only
result = prepare.protein("protein.pdb").fetch()

# Protein-ligand complex
result = prepare.protein_ligand("complex.pdb", ligand_names=["LIG"]).fetch()

class rush.prepare.ResultRef(models)

Bases: object

Lightweight reference to prepare-protein output in the Rush object store.

May contain multiple TRC triplets if the input PDB has multiple models.

Parameters:

models (list[TRCRef])

classmethod from_raw_output(res)

Parse raw collect_run output into a ResultRef.

The raw output is a list of groups, where each group is a list of 3 dicts (topology, residues, chains objects). Multi-model PDBs produce multiple groups.

Parameters:

res (Any)

Return type:

ResultRef

fetch()

Download prepare-protein output and parse into TRCs.

Returns one TRC per model in the input PDB. Most PDBs contain a single model, so result[0] is the common pattern.

Return type:

list[TRC]

save()

Download prepare-protein output and save to the workspace.

Returns one TRCPaths per model in the input PDB.

Return type:

list[TRCPaths]

models: list[TRCRef]

rush.prepare.protein(mol, ph=None, naming_scheme=None, capping_style=None, truncation_threshold=None, opt=None, debump=None, run_spec=RunSpec(gpus=1), run_opts=RunOpts())

Submit a prepare-protein job for a PDB or TRC file.

Returns a RushRun handle. Call .fetch() to get the parsed TRC, or .save() to write the output files to disk.

Parameters:

• mol (TRC | TRCRef | tuple[Path | str | RushObject | Topology, Path | str | RushObject | Residues, Path | str | RushObject | Chains] | Path | str)

• ph (float | None)

• naming_scheme (Literal['AMBER', 'CHARMM'] | None)

• capping_style (Literal['never', 'truncated', 'always'] | None)

• truncation_threshold (int | None)

• opt (bool | None)

• debump (bool | None)

• run_spec (RunSpec)

• run_opts (RunOpts)

Return type:

RushRun[ResultRef]

rush.prepare.protein_ligand(mol, ligand_names, ph=None, naming_scheme=None, capping_style=None, truncation_threshold=None, opt=None, debump=None, run_spec=RunSpec(gpus=1), run_opts=RunOpts())

Submit a complex preparation job for a PDB or TRC file.

Internally runs prepare-protein, extracts ligands, merges, and uploads the combined TRC. The returned RushRun wraps the prepare-protein job. Calling .fetch() or .save() blocks until the protein preparation completes, then performs the merge locally.

Returns a RushRun handle. Call .fetch() to get the parsed TRC, or .save() to write the output files to disk.

Parameters:

• mol (TRC | Path | str)

• ligand_names (list[str])

• ph (float | None)

• naming_scheme (Literal['AMBER', 'CHARMM'] | None)

• capping_style (Literal['never', 'truncated', 'always'] | None)

• truncation_threshold (int | None)

• opt (bool | None)

• debump (bool | None)

• run_spec (RunSpec)

• run_opts (RunOpts)

Return type:

RushRun[ResultRef]